Twisted Bacteria

Keeping harmful protein fibres at bay

noreply@blogger.com (César Sánchez) — Sun, 12 Aug 2012 23:31:00 +0000

Misfolded proteins are not just useless — they can be toxic. Some of them form linear aggregates known as amyloid fibres that can lead to disorders such as Alzheimer’s and Parkinson’s diseases. Writing in PLoS Biology, James Shorter and colleagues describe a protein machinery that inhibits the formation and helps to dissolve such fibres.

Heat shock proteins (HSPs) assist other proteins in folding. The authors set out to study whether two small HSPs from baker’s yeast (Hsp26 and Hsp42) could affect the generation of amyloid fibres by a misfolded protein of the same organism (Sup35). Using purified proteins, the researchers showed that Hsp26 and Hsp42 inhibited amyloid formation. Moreover, they determined exactly which steps of the process were affected: Hsp42 slowed down an early structural reorganization of small aggregates before the fibres were formed, whereas Hsp26 inhibited fibre growth.

Yeast cells have a protein called Hsp104 that rapidly dissolves amyloid. However, humans and other animals lack such an enzyme, and so it was unclear how our cells can get rid of amyloid fibres. The authors report that Sup35 fibres can be dissolved by a combination of several yeast HSPs (Hsp40, Hsp70 and Hsp110) in the absence of Hsp104, especially if the fibres are pretreated with Hsp26 and Hsp42. What’s more, they obtained similar results when using the equivalent human HSPs to disaggregate α-synuclein amyloid fibres, which are involved in Parkinson's disease. Although amyloid disassembly took many days, the researchers propose that such system could be functional in long-lasting cells such as neurons.

Shorter and colleagues’ findings suggest that enhancing the activity of certain HSPs in affected cells — and/or introducing yeast Hsp104 — could help to dissolve the amyloid in disorders such as Parkinson’s disease. However, additional research would be needed to assess the efficacy and safety of such potential treatments before these could be tested in people.

Reference (and source of the image):

Duennwald ML, Echeverria A, Shorter J (2012). Small Heat Shock Proteins Potentiate Amyloid Dissolution by Protein Disaggregases from Yeast and Humans. PLoS Biol, 10(6): e1001346. DOI: 10.1371/journal.pbio.1001346

Social media tools and academic publishing, a presentation by Alan Cann

noreply@blogger.com (César Sánchez) — Sat, 09 Jun 2012 19:02:00 +0000

The following video is a presentation by Alan J. Cann for Editing in the Digital World, 11th EASE General Assembly and Conference Tallinn, Estonia, 8-10 June 2012.

Abstract of the presentation as published in the conference programme:

Social media tools and academic publishing
Alan J. Cann, Internet Consulting Editor, Annals of Botany; Department of Biology, University of Leicester, Leicester, UK
As publishing moves from print-focused (slow, inflexible, expensive) to content-focused (digital delivery, article-level metrics/discussion), there is an increasing need for publishers to communicate with their audiences in ‘adjacent spaces’ beyond the traditional medium of the journal or book. Social technologies will continue to evolve rapidly for the foreseeable future, so publishers need to acquire sufficient expertise to remain agile in this area in the face of future developments. I will describe the Annals of Botany low-cost online social media strategy, which is extending the reach of the journal to new audiences and new demographic groups. This includees blogs as distribution hubs for content via RSS, Twitter and Facebook, and emerging tools such as Flipboard which allow content discovery on new platforms such as tablet computers.

And here you have a link to the AoB Blog.

Microbiology blogs: a list of 20 great blogs for microbe lovers

noreply@blogger.com (César Sánchez) — Thu, 01 Sep 2011 14:40:00 +0000

Bertalan Meskó (@Berci) has compiled a list of microbiology blogs that you may find useful: Microbiology in the Blogosphere.

Envious, I decided to make my own list of microbiology blogs. After checking my Google Reader, I came up with a collection of 20 great blogs. I know there are many more out there, so please feel free to add a comment and suggest any microbiology blogs that may be missing from my list.

So, here they come, in strict alphabetical order:

1 - Aetiology by Tara C. Smith (@aetiology): "Discussing causes, origins, evolution, and implications of disease and other phenomena."

2 - Bactérioblog [in French] by Benjamin (@bacterioblog):"Le blog des bactéries et de l'évolution".

3 - BacterioFiles by Jesse Noar (@BacterioFiles): "The podcast for microbe lovers: reporting on exciting news about bacteria, archaea, and sometimes even eukaryotic microbes and viruses".

4 - Cornell Mushroom Blog by a collective of faculty, staff and students from Cornell University: "Even in the fullness of their horrific evilness, fungi are cool. That’s what we’re all about here."

5 - Curiosidades de la Microbiología [in Spanish] by Manuel Sánchez (@Manuel_SanchezA) (no relation!): "Este blog está dedicado a la Microbiología pero en general cualquier tema científico de interés tambien puede aparecer".

6 - Life of a Lab Rat ("occasional insights into the life of a lab rat") and Lab Rat ("Exploring the life and times of bacteria") by S. E. Gould (@labratting).

7 - Memoirs of a Defective Brain by The Defective Brain: "Science as told by malfunctioning neurones. A blog of Life, labs and bacteria."

8 - Microbichitos [in Spanish] by Miguel Vicente: "Los microbios no los vemos, pero sus efectos, para bien o para mal nos afectan a diario." Previously, Miguel used to blog at Esos pequeños bichitos.

9 - MicrobiologyBytes by Alan Cann (@MicroBytes): "The latest news about microbiology".

10 - MIKROB(io)LOG [in Slovenian] by Franc Nekrep (@fvnek): "srečevali se bomo mikrobiologi: študenti, učitelji, kolegi iz stroke pa seveda VSI LJUDJE DOBRE VOLJE..."

11 - MycoRant by Philip McIntosh (@MycoRant): "Philip has been writing, researching, publishing and doing other things in the realm of fungi since 1993".

12 - Mystery Rays from Outer Space by Ian York (@iayork): "This blog is intended to be a place for commentary on immunology, virology, and random other stuff that catches my eye."

13 - Skeptic Wonder ("protists, memes and random musings") and The Ocelloid ("Through the eye of a microbe") by Psi Wavefunction (@PsiWavefunction).

14 - Small Things Considered by Elio Schaechter, Merry Youle and collaborators: "The purpose of this blog is to share my appreciation for the width and depth of the microbial activities on this planet".

15 - The Artful Amoeba by Jennifer Frazer (@JenniferFrazer): "a blog about the weird wonderfulness of life on Earth". Older posts can be found here.

16 - The Febrile Muse by CMDoran (@TheFebrileMuse): "Portrayal of Infectious Diseases in Literature and the Arts".

17 - The Gene Gym by Jim Caryl (@mentalindigest): "Bad bugs, drugs and antibiotic resistance, all in a day's work at The Gene Gym, brought to you from the gym floor by a researcher (fitness instructor) in bacterial evolution".

18 - The Tree of Life by Jonathan Eisen (@phylogenomics), "evolutionary biologist, microbiologist and genomics researcher, Open Access and Open Science advocate".

19 - ViroBlogy by Ed Rybicki (@edrybicki): "Up-to-date Virology-related posts, mainly for students at the University of Cape Town".

20 - Virology blog by Vincent Racaniello (@profvrr): "about viruses and viral disease".

Note: I don't speak French or Slovenian, but that's what Google Translate is for, isn't it?

Cornering multiple sclerosis -- still a long way to go

noreply@blogger.com (César Sánchez) — Thu, 25 Aug 2011 09:15:00 +0000

Multiple sclerosis is an autoimmune disease of the central nervous system that causes neurological disability in young adults. Several environmental and genetic factors have been linked to the disease, but the precise mechanisms involved, and whether neurological damage precedes inflammation or vice versa, remain unclear.

In a recent article published in Nature, an international consortium of researchers report the identification of 29 new susceptibility loci, most of which are related to immune system function and, in particular, to T-helper-cell differentiation.

Previous genome-wide association studies (GWAS) that analysed relatively modest numbers of multiple sclerosis patients identified more than 20 risk loci, especially some that encode components of the major histocompatibility complex (MHC). To identify a more complete set of susceptibility loci and obtain new insights into disease mechanisms, an international team of researchers carried out a large GWAS in which they analyzed over 465,000 autosomal single nucleotide polymorphisms (SNPs) from about 9,800 patients and 17,400 controls (that is, people not affected by multiple sclerosis) from 15 countries.

This analysis confirmed 23 loci that had previously been linked to the disease, and revealed another 29 new loci. Most of the risk attributable to the MHC could be accounted by four mutations, one in class-I locus HLA-A and three in class-II locus HLA-DRB1.

A statistical analysis of the functions of the 52 loci (as annotated in the Gene Ontology database) showed that they are enriched for lymphocyte functions. In particular, many genes encoding cell surface receptors (such as CXCR5 and IL7R) with roles in T-helper-cell differentiation showed strong association with multiple sclerosis. In addition, the researchers identified two susceptibility loci with a role in vitamin D synthesis (CYP27B1 and CYP24A1) and others that encode known targets of therapies for multiple sclerosis such as natalizumab (VCAM1) and daclizumab (IL2RA). By contrast, very few genes with known roles in inflammation-independent neurodegeneration were identified.

The overrepresentation of susceptibility genes with roles in T-cell maturation suggests that multiple sclerosis is primarily caused by immune dysfunction, which is followed by neurological damage. However, the 52 variants can explain only ~20% of the heritability of the disease, and therefore a myriad of other susceptibility loci, each adding a tiny percentage to the overall risk of developing multiple sclerosis, remain to be identified.

Original article:
The International Multiple Sclerosis Genetics Consortium & The Wellcome Trust Case Control Consortium 2 (2011). Genetic risk and a primary role for cell-mediated immune mechanisms in multiple sclerosis Nature, 476 (7359), 214-219 DOI: 10.1038/nature10251

The same story in the news:
- Study identifies 57 genes linked with MS, Multiple Sclerosis Society, UK (10 Aug 2011).
- Multiple sclerosis genes identified in largest-ever study of the disease by Alok Jha, The Guardian (10 Aug 2011).
- Scientists unravel genetic clues to multiple sclerosis by Kate Kelland, Reuters (10 Aug 2011).

Note:
During the last 10 months, I have written 18 Research Highlights (short pieces of 300-400 words that summarize recent scientific articles) for Nature Reviews Microbiology. This blog post is based on my first attempt to write a similar piece about a non-microbiological article. However, to make the post more 'blog-friendly', I have embedded some links to definitions of key terms. You can read the definitions by rolling your mouse over the highlighted terms, or you can click on the term to visit a website with more information. Also, I have added a couple of links to news articles that covered the same story.

Time-lapse photography of growing mould - Amazing video!

noreply@blogger.com (César Sánchez) — Mon, 24 Jan 2011 07:59:00 +0000

Please watch the following video made by Nick Lariontsev, and then let me know if you don't think that microbes are fascinating things.

The video was made using time-lapse photography, with several fungi as 'actors': apparently, Aspergillus fumigatus, Botrytis, Mucor, Trichoderma and Cladosporium. You can see several pictures of the device used to take the photos at Nick's LiveJournal. See, for instance, this one (photo courtesy of Nick Lariontsev):

I found the video via The Microbiology Daily (a Twitter newspaper) <<< @KristaMarquis (Twitter) <<< MicroCulture (Tumblr) <<< Fungi (Tumblr) <<< Interact With (Tumblr) <<< YouTube <<< Nick (LiveJournal).

Microbes rule!!

Want to have some fun? Do some peer reviewing for a scientific journal!

noreply@blogger.com (César Sánchez) — Sat, 11 Dec 2010 12:36:00 +0000

Every December, the journal Environmental Microbiology publishes a collection of humorous quotes made by peer reviewers while assessing manuscripts submitted to the journal. Some of them are hilarious! I am extracting a few of them from the last two years, but I recommend reading them all!

Here you go:

Desperate referees:

This paper is desperate. Please reject it completely and then block the author’s email ID so they can’t use the online system in future.

The biggest problem with this manuscript, which has nearly sucked the will to live out of me, is the terrible writing style.

The writing and data presentation are so bad that I had to leave work and go home early and then spend time to wonder what life is about.

The finding is not novel and the solution induces despair.

Desperate authors:

WOW! You did ‘read it with interest’ in SEVEN MINUTES??!! [Ed.: this is an author contribution in response to an editorial decision (rejection) made within 7 min of submission]

Holiday season:

Done! Difficult task, I don’t wish to think about constipation and faecal flora during my holidays!

The peaceful atmosphere between Christmas and New Year was transiently disrupted by reading this manuscript.

Merry X-mas! First, my recommendation was reject with new submission, because it is necessary to investigate further, but reading a well written manuscript before X-mas makes me feel like Santa Claus.

Season’s Greetings! I apologise for my slow response but a roast goose prevented me from answering emails for a few days.

Technical issues:

[...] maybe some beetle took a pee on one or the other of the samples [...]

You call the sample fresh water, this is confusing as it is saline water.

The trees are crap but, besides this, excellent work.

Writing style:

You know there is something important there but the language is so inaccessible that you cannot make up your mind if they are trying to hide something or they actually think that is a good style of writing.

This manuscript gets the title ‘worst written manuscript of the year reviewed by DJ’

The writing style is flowery and has an air of Oscar Wilde about it.

Great manuscripts:

This is a long, but excellent report. [...] It hurts me a little to have so little criticism of a manuscript.

I perused this manuscript while in the hotel prior to a friend’s wedding. I was suspicious that a state of relaxation had influenced my enjoyment of a paper on soil formation; so I read it again, this time squashed between two large people on the delayed flight home, and still enjoyed reading it.

Very much enjoyed reading this one, and do not have any significant comments. Wish I had thought of this one.

It is always a joy to review manuscripts such as this. Well-conceived, well executed, well edited. Clean. Pristine. From start to finish.

Links:
- Referees' quotes – 2010. Environmental Microbiology (2010) 12, 3303–3304.
- Referees' quotes – 2009. Environmental Microbiology (2009) 11, 3309–3310.

Image credits:
Image (desperate schoolboy) modified from a photo by Patrick Bell. Source: Flickr. This image is licensed under a Creative Commons Attribution 3.0 Unported License.

Microbial pigments: an untapped resource for teachers, artists and researchers

noreply@blogger.com (César Sánchez) — Wed, 06 Oct 2010 11:42:00 +0000

The journal PLoS Biology has launched a new series of articles on education "to present innovative approaches to teaching critical concepts, developments, and methods in biology." The title of the first article in the series is In Living Color: Bacterial Pigments as an Untapped Resource in the Classroom and Beyond.

From the article:

"Soil bacteria from the Streptomyces genus represent a source of interesting natural products that have been largely overlooked by artists, researchers, and teachers. This article is intended to encourage amateurs and professionals alike to explore this overflowing source of biopigments. Not only does this endeavor have the potential to lead us toward a fertile nexus between art and science, it may also lead to a more sustainable and environmentally friendly way to color the world around us in the future. The relevance of biopigments to many facets of science, technology, and society, makes this material an outstanding tool to engage students of varying academic interests across multiple age groups. Therefore, we encourage teachers of all levels to consider using biopigments as a vehicle to introduce the scientific method to their students. To facilitate the implementation of biopigments into science and art curricula, we have provided a list of useful online resources and information about procuring materials [...] as well as recommend ways to evaluate the effectiveness of the lesson [...]."

Original article (and image source):
Charkoudian LK, Fitzgerald JT, Khosla C, Champlin A (2010) In Living Color: Bacterial Pigments as an Untapped Resource in the Classroom and Beyond. PLoS Biol 8(10): e1000510. doi:10.1371/journal.pbio.1000510
Image: “Elvis Lives!” painted on agar media plates using the bacterium Streptomyces coelicolor.

Related links:
- Microbial Art, a collection of unique artworks created using living bacteria, fungi, and protists.
- Painting With Penicillin: Alexander Fleming's Germ Art. The scientist created works of art using microbes, but did his artwork help lead him to his greatest discovery? By Rob Dunn. Smithsonian.com, July 12, 2010.
- Streptomyces: they're twisted! Twisted Bacteria, Aug 10, 2007.

A voyage from molecular genetics to microbial ecology -- includes a fish tank and some cartoons

noreply@blogger.com (César Sánchez) — Thu, 19 Aug 2010 11:15:00 +0000

The March issue of International Microbiology included a very nice article by Roberto Kolter, professor of Microbiology and Molecular Genetics at Harvard Medical School. The title is Biofilms in lab and nature: a molecular geneticist’s voyage to microbial ecology (freely available as PDF).

In the article, the author gives an entertaining account of the path that lead him to the study of biofilms -- that is, aggregations of microbes growing on solid substrates. He also highlights some of his recent research on the ecology of microbial islands.

There is also a fish tank anecdote. And I added a couple of microbial cartoons, just for fun!

Microbes are excellent model organisms... at least for studies on basic cellular processes. As Jacques Monod put it: Ce qui est vrai pour le colibacille est vrai pour l’éléphant ("what is true for the colibacillus is true for the elephant"). That is why Roberto Kolter (and many other researchers) soon fell under the spell of bacteria and, in particular, the colibacillus Escherichia coli.

For some time, Kolter studied the regulation of cell growth in E. coli. Under the right conditions, cells divide to yield daughter cells, which grow and divide quickly again, and so on -- and the bacterial population undergoes exponential growth. This exponential phase of growth (a.k.a. log phase) is typically followed by a stationary phase, when the growth rate slows down due to a scarcity of nutrients and accumulation of toxic products. Eventually, the bacterial population shrinks, in what is known as death phase (you can visit Cells alive! or Wikipedia for basic information on bacterial growth).

These processes are typically studied in the laboratory using shaken cultures. The shaking of flasks and test tubes keeps the broth composition uniform throughout the flask, and provides a continuous supply of fresh air that helps microbes grow fast. As a result, the cells are in a planktonic state; that is, they grow in suspension in the broth.

From these shaker-sick cultures, Kolter and coworkers learnt a few interesting things about what happens during the stationary and death phases. In the International Microbiology article, he summarizes their findings as follows:

"And what we found through genetic analyses was rather extraordinary. Death allowed new life; we were witnessing evolution in real time [...]. Underlying the usually observed death phase was a dynamic world of dying and growing bacteria. There were constant population takeovers such that pre-existing fitter bacterial mutants grew as the original population met its demise. Evolutionary cheating we would call it later on [...]"

In other words, the adverse conditions occurring in the E. coli cultures during the death phase (toxic products, little food) appeared to have two contrasting effects. It was obvious that many cells were dying -- but, at the same time, successive waves of different spontaneous mutants were able to thrive and outgrow their dying siblings in this less-than-optimal environment. These findings were reviewed in two papers with memorable titles: Life after log and GASPing for life in stationary phase.

Isn't that a fascinating microcosms? The little creatures in the test tube were not just dying; they were evolving!

And now, the fish tank anecdote. Or, in Kolter's own words, the epiphany of the fish tank:

"The years that followed represented for me a dramatic turn of direction in my research. One might ascribe the change to some sort of “post-tenure depression”; I refer to it as the “epiphany of the fish tank” now. [...]
Microbial life on surfaces, for decades studied by Bill Costerton and other intrepid pioneers of the biofilm field, had been long ignored by most microbial physiologists and molecular geneticists, myself included. However, things changed for me in 1994 when, noticing my depressed state, members of my laboratory gave me a fish tank in a effort to draw me out of the blues. As I sat locked-up in the office staring at the tank, I realized that by studying shaken cultures of E. coli I had been barking up the wrong tree. The water in the fish tank remained crystal clear, it was on the surfaces where most microbial activity was occurring."

That observation applies well beyond fish tanks. It is possible that the majority of microbes on Earth spend most of their lives in aggregates attached to surfaces, and therefore not in a free-floating or swimming, planktonic state. Obviously, they are not solitary guys: we could view biofilms in nature as quite complex 'societies' or 'cities' where different types of microorganisms inhabit buildings made out of sticky macromolecules (polysaccharides, proteins, DNA). Importantly, microbes in biofilms are sometimes resistant to the action of antibiotics, to which the same organisms are sensitive when in planktonic state.

So, have microbiologists been "barking up the wrong tree" all this time? Well, not exactly. Experiments using shaken cultures have been, and will continue to be, extremely useful. They are, without doubt, highly valuable to learn about the biochemistry, genetics and many other aspects of the biology of microbes. And they have been instrumental in providing us with antibiotics and vaccines to fight infectious disease.

But it is true that shaken cultures are sometimes not the best research models, especially if we try to understand 'the real life' of a microbe in its natural environment.

The 'fish tank epiphany' lead Kolter into biofilm research. A first approach he and his collaborators took was to study the biofilms formed by certain Bacillus subtilis strain. The accompanying image shows --on the left-- a beaker with a floating film that the microbe forms when grown in a standing (not shaken!) liquid culture, and --on the right-- a magnified view of a colony grown on an agar plate. Although these biofilms consist only of a single organism, they are actually highly structured, with several layers composed of different cell types engaged in various activities: some cells are actively producing the matrix (not the Wachowskis' movie but the glue that keeps the biofilm together), others are swimming around, and there are also some cells in the process of becoming spores. How close is that to a multicellular organism?

The B. subtilis biofilm is a very useful model -- but you may well think that a beaker containing a single microbial species is a very artificial setting.

Then, how can scientists study biofilms in natural environments? For Kolter, the inspiration came -- no fish tank involved -- from the writings of biologist E. O. Wilson. In collaboration with Robert MacArthur, Wilson developed in the 1960s the theory of island biogeography, which has become fundamental in ecology and evolutionary biology. The theory tries to explain the factors that control the number of species in a natural community (it was originally developed for islands but now it is applied to any ecosystem that is surrounded by other ecosystems). Kolter was fascinated by the ways Wilson studied newly formed islands to put the theory to the test (what Wilson actually did was to fumigate some small islands to kill all arthropods, and then observe how the islands were recolonized). However, Kolter was wise enough and did not try to make free from microbes any islands (that would be tough!). His approach, much less destructive, consisted of studying two natural microbial islands: the pitchers of a carnivorous plant, and the human lungs.

The first island is Sarracenia purpurea, a carnivorous plant feeding on the insects and spiders that fall into its water-filled pitchers. Kolter and collaborators found that the inside of unopened, newly formed pitchers was sterile -- there you go, a microbial island is born! This allowed them to analyse the composition of the nascent bacterial population in the pitchers during the season, as microbes colonized the island. Among other results, the researchers found that pitchers containing certain mosquito larvae (keystone predators) had a greater bacterial diversity.

The second microbial island studied by Kolter and coworkers is the respiratory tract of humans suffering from cystic fibrosis (CF). As long as you are healthy, your lungs are supposed to be mostly sterile. However, respiratory diseases such as CF or asthma open the gates to outside microbial colonizers, which can make a lot of harm. In CF, the major microbial pathogen is the bacterium Pseudomonas aeruginosa, which forms biofilms inside the lungs and can easily become resistant to antibiotics. Using culture-independent methods, Kolter's laboratory compared the microbial communities in the lungs of different CF patients. The researchers showed that the presence of P. aeruginosa was correlated with lower microbial diversity, worse lung function, and patient age. In other words, it appears that the arrival of P. aeruginosa (an 'invasive species') greatly affects the microbial community in CF lungs, resulting in a decrease in diversity. The researchers suggest that the composition of the microbial community could be a better predictor of disease progression than the presence of P. aeruginosa alone.

Well, that was a long post. Please read Roberto Kolter's article (it is free), which includes a few more interesting thoughts and quotes. The concept of microbial islands is fascinating. And the growing interaction between the long-time isolated fields of ecology and microbiology is, I think, changing the way microbiologists view their study subjects. Hopefully, ecologists will also become more aware of the organisms that rule the planet -- which are not humans, you know.

Reference for Roberto Kolter's article:
Roberto Kolter (2010). Biofilms in lab and nature: a molecular geneticist’s voyage to microbial ecology. Int. Microbiol., 13, 1-7. DOI: 10.2436/20.1501.01.105 (pdf)

Related links:

- Biology of microbial communities - Interview to Roberto Kolter (video). JoVE, May 2007.

- Roberto Kolter - Bacillus subtilis and bacteria as multicellular organisms (podcast). Meet the Scientist, episode 20, March 2009. MicrobeWorld.

- The evolution of the biofilm concept: a long and winding road (free PDF), by J.W. Costerton. Sartoniana (2008) 21:59-67.

- About the existence of microbes (viruses) in healthy and diseased human lungs: Metagenomic Analysis of Respiratory Tract DNA Viral Communities in Cystic Fibrosis and Non-Cystic Fibrosis Individuals (2009). PLoS ONE 4(10): e7370. doi:10.1371/journal.pone.0007370 (free article).

Image credits:

- Cartoons by Sanja Saftic. Many thanks to her for allowing me to use the cartoons for this blog post. Source: Biotoon.com - Microbiological Edutainment.

- Color-enhanced scanning electron microscope (SEM) image of a biofilm formed by Desulfovibrio desulfuricans bacteria. Image by PNNL - Pacific Northwest National Laboratory. Source: Flickr.

- Beaker and colony: highly structured biofilms formed by Bacillus subtilis strain NCIB 3610. Source: International Microbiology.

- Sketch of carnivorous plant: Sarracenia purpurea. Source: Wikimedia Commons.

They Might Be Giants: Science is Real - a music video

noreply@blogger.com (César Sánchez) — Fri, 25 Jun 2010 12:25:00 +0000

Via my Daily on Twitter >>> Michael Banks (Twitter) >>> Rocking the physics message (physicsworld.com) >>> They Might Be Giants (ParticleMen, YouTube).

TED videos: excellent talks about life, the universe and everything -- including microbes

noreply@blogger.com (César Sánchez) — Tue, 22 Jun 2010 11:20:00 +0000

TED is a nonprofit organization devoted to "ideas worth spreading." They are mostly known because of their growing collection of fascinating talks about a wide array of topics, including science, art and anything in-between (or around). The talks are recorded and the videos are freely available at their website, where you can also find information about the speakers and interactive transcripts (including translations to various languages).

In this post I'm collecting links to all the TED videos I could find related to the microbial world.

Topics include: life in the deep oceans, medical mysteries, bacterial Esperanto, predicting pandemics, robots turned into microbiologists, new approaches to handle infectious diseases, looking for life on Mars and beyond, fungi that could save the world, bacteria that may have caused mass extinctions...

Awesome, huh?

I'm also embedding a video for one of the latest TED talks: Seth Berkley: HIV and flu -- the vaccine strategy. The speaker, epidemiologist Seth Berkley, is the founder of the International AIDS Vaccine Initiative. In this talk, filmed last February, he spoke about new methods for making vaccines for AIDS and flu.

I also recommend reading this interview on the TED blog, where Seth Berkley commented on the same subject. I am copying here a few remarkable quotes:

I was very disappointed by public concerns that we ordered too much flu vaccine and that some might get wasted. (...) I think that both declaring this a global pandemic and accelerating vaccine production as quickly as possible were the right decisions. If you want to prepare a population for an emergency it means that you might ultimately spend some money that isn’t used.

That's a good point. Many criticisms have been raised in the last months against WHO decisions in relation to the recent flu pandemic. And some of those criticisms were undeserved, in my opinion.

In the interview, Berkley explained why so much effort was put on developing treatments --rather than preventive vaccines-- for AIDS. And he described the extraordinary work they're doing with the International AIDS Vaccine Initiative.

To the question "Are the members of the younger generation of scientists as invested in creating a vaccine as was the case 10 years ago or so?" he responded:

Sadly not. (...) The problem is not that young scientists don’t think vaccines are incredibly important, the problem is that it is seen as such a difficult problem, such a long-term problem that what they’re worried about is: Can they build a career on it? Can they get the types of breakthroughs they need in a rapid time frame that would make it a productive place to work?

It is disturbing that the "productivity" concept not only is doing harm to many researchers' careers but may also be slowing down the development of much-needed medical treatments...

Why not focus just on the treatment of infected people, and forget about an AIDS vaccine? Berkley explained:

(...) from a public policy point of view, there’s great expense involved in dealing with the epidemic through treatment and reaching people when they’re already infected. (...) But this is a long-term entitlement program, because once you put somebody on treatment, they have to get treatment for the rest of their lives and they develop conditions, they develop toxicity and they need other treatments. So, there’s almost a sense now that all of the bright lights of that unbelievable effort -- the unprecedented emergency program for AIDS relief, Bush’s triumph that people look on as being a great thing that he did, will create a demand that gets higher and higher and higher just to keep up with where we are.

So, making an effective vaccine against AIDS may be very difficult. But it is worth the effort.

And finally, as promised, this is the list of other TED videos related to the small living beings (in chronological order, newest first):

[Added October 15th, 2010 -- Eben Bayer: Are mushrooms the new plastic? "Product designer Eben Bayer reveals his recipe for a new, fungus-based packaging material that protects fragile stuff like furniture, plasma screens -- and the environment." July 2010. Found via MicrobiologyBytes.]

Magnus Larsson: Turning dunes into architecture. "Architecture student Magnus Larsson details his bold plan to transform the harsh Sahara desert using bacteria and a surprising construction material: the sand itself." July 2009.

Nathan Wolfe: hunting the next killer virus. "Virus hunter Nathan Wolfe is outwitting the next pandemic by staying two steps ahead: discovering deadly new viruses where they first emerge -- passing from animals to humans among poor subsistence hunters in Africa -- before they claim millions of lives." February 2009.

Bonnie Bassler: discovering bacteria's amazing communication system. "Bonnie Bassler discovered that bacteria "talk" to each other, using a chemical language that lets them coordinate defense and mount attacks. The find has stunning implications for medicine, industry -- and our understanding of ourselves." February 2009.

Hans Rosling on HIV: New facts and stunning data visuals. "Hans Rosling unveils new data visuals that untangle the complex risk factors of one of the world's deadliest (and most misunderstood) diseases: HIV. He argues that preventing transmissions -- not drug treatments -- is the key to ending the epidemic." February 2009.

Kary Mullis' next-gen cure for killer infections. "Drug-resistant bacteria kills, even in top hospitals. But now tough infections like staph and anthrax may be in for a surprise. Nobel-winning chemist Kary Mullis, who watched a friend die when powerful antibiotics failed, unveils a radical new cure that shows extraordinary promise." February 2009.

James Nachtwey fights XDR-TB. "Photojournalist James Nachtwey sees his TED Prize wish come true, as we share his powerful photographs of XDR-TB, a drug-resistant strain of tuberculosis that's touching off a global medical crisis. Learn how to help at http://www.xdrtb.org" October 2008.

Paul Stamets: six ways mushrooms can save the world. "Mycologist Paul Stamets lists 6 ways the mycelium fungus can help save the universe: cleaning polluted soil, making insecticides, treating smallpox and even flu." March 2008.

Peter Ward: Earth's mass extinctions. "Asteroid strikes get all the coverage, but "Medea Hypothesis" author Peter Ward argues that most of Earth's mass extinctions were caused by lowly bacteria. The culprit, a poison called hydrogen sulfide, may have an interesting application in medicine." February 2008.

Paul Ewald: can we domesticate germs? "Evolutionary biologist Paul Ewald drags us into the sewer to discuss germs. Why are some more harmful than others? How could we make the harmful ones benign? Searching for answers, he examines a disgusting, fascinating case: diarrhea.". March 2007. (I embedded this video in a previous post.)

Bill Stone explores the world's deepest caves. "Bill Stone, a maverick cave explorer who has plumbed Earth’s deepest abysses, discusses his efforts to mine lunar ice for space fuel and to build an autonomous robot for studying Jupiter’s moon Europa." "How do you take a robot and turn it into a field microbiologist?" March 2007.

Laurie Garrett on lessons from the 1918 flu. "In 2007, as the world worried about a possible avian flu epidemic, Laurie Garrett, author of "The Coming Plague," gave this powerful talk to a small TED University audience. Her insights from past pandemics are suddenly more relevant than ever." February 2007.

Penelope Boston says there might be life on Mars. "So the Mars Rovers didn't scoop up any alien lifeforms. Scientist Penelope Boston thinks there's a good chance -- a 25 to 50 percent chance, in fact -- that life might exist on Mars, deep inside the planet's caves. She details how we should look and why." February 2006.

Larry Brilliant wants to stop pandemics. "Accepting the 2006 TED Prize, Dr. Larry Brilliant talks about how smallpox was eradicated from the planet, and calls for a new global system that can identify and contain pandemics before they spread". February 2006.

Joe DeRisi solves medical mysteries. "Biochemist Joe DeRisi talks about amazing new ways to diagnose viruses (and treat the illnesses they cause) using DNA. His work may help us understand malaria, SARS, avian flu -- and the 60 percent of everyday viral infections that go undiagnosed." February 2006.

David Gallo on life in the deep oceans. "With vibrant video clips captured by submarines, David Gallo takes us to some of Earth's darkest, most violent, toxic and beautiful habitats, the valleys and volcanic ridges of the oceans' depths, where life is bizarre, resilient and shockingly abundant." February 1998.

Live webcast & Twitter: great combination for scientific conferences

noreply@blogger.com (César Sánchez) — Fri, 18 Jun 2010 17:39:00 +0000

As I mentioned in my previous post, thanks to the internet, I could peek into the meeting of the American Society for Microbiology (ASM), recently held in California, from the comfort of my home at London, UK. This was possible because some of the meeting attendees posted comments on Twitter, in real time, and also because the meeting organizers made a live video broadcast available to everyone through the internet (that is, a webcast).

The webcast, called ASM Live, consisted of nine interviews to researchers on their latest findings. The interviews were very aptly handled by Jeff Fox, Features Editor for Microbe Magazine (a freely available, monthly magazine published by the ASM). Moreover, viewers were allowed to submit questions to the researchers by either using the online chat (provided by UStream) or tweeting to @MicrobeWorld.

Two of the most popular interviews seemed to be The Gulf oil spill: microbes to the rescue? and The first synthetic genome: what does this mean for microbiology, and for everybody else?? [note that there were two question marks in the original title, and this is not necessarily a typo :) ]

All the interviews were really interesting -- and you can still watch them: they are archived at MicrobeWorld (an online community for sharing multimedia resources related to microbiology) and UStream.tv (the live interactive broadcast platform that was used for the ASM webcast).

My sincere congratulations to everybody involved in the making and broadcasting of the interviews, that was a great piece of work!

And now, let's focus on Twitter.

About 1,200 messages containing the #asmgm hashtag were posted to Twitter in relation to the ASM meeting. There were all kinds of messages, and many of them were informative, insightful, or funny. Some of them included links to interesting articles or websites, while others redirected to photos captured during the meeting. I mentioned a couple of popular tweets in a previous blog post, and I'm including here a few more as illustrations.

However, if you search for the #asmgm hashtag on Twitter, you will only get recent messages posted during the last 7-10 days -- which is really disappointing.

Luckily, Alan Wolf had the brilliant idea of creating an archive for #asmgm tweets on Twapper Keeper. The archive is freely available online, so anybody can read and download all the messages.

In addition to archiving, there are other ways of reading 'old' Twitter messages: for instance, I find Topsy quite useful. However, archiving seems a very sensible idea to me -- especially for scientific conferences.

[Note: Twapper Keeper can only reach back as far as Twitter allows, so the archive needs to be started as soon as possible (ideally a few days before the conference, to include any pre-meeting tweets)]

Once the ASM meeting was over, I thought that a word cloud, as a visual representation of 'hot topics' (the most tweeted), could be a nice illustration for a blog post. So, I searched the internet looking for a suitable, user-friendly online tool that would generate -- automagically -- the perfect word cloud for me. But I did not find it.

After a trial-and-error process, I finally made a nice-looking cloud (which was featured image of the week at MicrobeWorld) using Wordle, but the result wasn't exactly what I had in mind:

Why wasn't I fully satisfied with my cloud? Firstly, because I had to do a lot of manual editing of the tweets: removing highly repetitive terms (such as "#asmgm", "RT"), fixing typos, stemming (a little), putting some words together to create meaningful tags (e.g. "San-Diego")... Also, the cloud was colourful and nice-looking, but the words were not individually hyperlinked (as in most tag clouds, see for instance the cloud located at the upper right side of my blog).

[Note: a tweetup is a meeting of two or more people who know each other through Twitter]

There are some online tools to generate tag clouds from Twitter messages. For instance, Tweetcloud seems to get quite close to what I have in mind. It indeed generates a tag cloud for a specific keyword (or user). But it seems to be limited by the Twitter search function (it only uses messages posted in the last 7-10 days). So, I guess I could have used this tool the day after the ASM meeting to create a cloud... but I didn't known about Tweetcloud at the time. Still, the cloud is not customizable at all.

So, I want to finish this post summarizing the characteristics of what I think would be an ideal tool to create word clouds from Twitter messages:

A) General

Freely available, online tool.

It could make a cloud for a hashtag, a word, a term composed of several words, or a Twitter user.

B) Searching Twitter

It wouldn't be limited by the 7-10 days boundary of the present search function of Twitter.

It would provide options to define specific limits for time (e.g. "only tweets posted between two given dates") and number of tweets ("only the last 100 tweets").

Options to exclude, or include, certain types of messages (replies, retweets, containing links, linking to images, linking to videos) or users ("exclude these users").

C) Creating the cloud

Options to use only hashtags (similar to My Tweet Cloud), exclude particular words (common words, numbers), use only particular types of words (e.g. nouns?).

Stemming.

It would detect possible typos, showing a list of candidates to be fixed. The user would decide if they should be corrected or not.

It would suggest possible tags composed of more than one word (e.g. "San" and "Diego" are always found together, do you want the tool to combine them into a single tag "San Diego"?). The user would decide.

The tags in the cloud should be hyperlinked. That is, clicking on a term such as "San Diego" would redirect to a list of tweets that included such a term.

D) Customizing the aspect of the cloud

Options to change the colour and relative orientation of tags, and the general aspect of the cloud (similar to Wordle).

Options to create an animated cloud showing changes in time (or location, user, etc). For instance, several clouds could be generated for a hashtag for different days (similar to this example) and could be combined into a single animated cloud. The user would define the period used to create each 'sub-cloud' (e.g. every day, every 6 hours) and the number of clouds needed for a smooth animation.

Please leave your comments, ideas or suggestions on creating Twitter tag clouds, or on the use of live webcast and Twitter for scientific conferences.

Note added on June 23rd:
I just read a great article on this topic: Twitterpated: Using Social Media at Academic Conferences. I found it via Hacking the Academy, a book that was crowdsourced on Twitter in one week. It deals with online education, scholarly communication and much more.

Related links:

- Added July 3rd: How to create a PDF archive of hashtagged tweets by Andrew Spong, STweM. It describes a simple workflow for archiving conference tweets. Found via FriendFeed.

- Added August 15th: SfN the Meh by DrugMonkey. Advice to the Society for Neuroscience (and other scientific societies): how to use social media for your next conference.

- Added August 22nd: Tagxedo - Tag Cloud with Styles. Tagxedo turns any word set (texts, blogs, tweets) into a visually appealing tag cloud. The cloud can fit a predetermined shape or silhouette. Link found via Andrew Spong's FriendFeed.

- Added September 4, 2010: Summarizr is a service that creates "a brief summary of a Twapper Keeper tweet archive. It works for #hashtag archives, keyword archives and @person archives. Just enter a hashtag, keyword, Twitter account name or archive URL in the form". See Twitter usage at the ASM meeting, based on TwapperKeeper archive of hashtag #asmgm.

Highlights from a scientific conference, observed via Twitter - #asmgm

noreply@blogger.com (César Sánchez) — Mon, 07 Jun 2010 16:55:00 +0000

Lots of conferences and meetings on science-related topics are held every year, all over the world. Many of them cover wide topics with potential to excite the curiosity of a great number of scientists and --more importantly-- common people. Sometimes, a few highlights of a conference are reported by the mass media, and that's good...

...but wouldn't it be even better if anybody could catch a glimpse of a particular conference, in real time? What about getting comments made by some of the attendees about a talk that is happening right now? And, what if the speaker could answer, in real time, a question asked by anybody from anywhere in the world?

Well, this is already happening, thanks to the internet!

In this blog post and an upcoming one, I'll describe some examples on how social media and other internet tools were used during a recent meeting of the American Society for Microbiology.

If you keep reading, you might learn a couple of interesting things about microbes. I also hope that these blog posts may give us all some food for thought about possible, better uses of the internet (and, in particular, social media) for the communication of science.

I'll be waiting for your comments, so don't be shy, I'm learning here!

The American Society for Microbiology (ASM) is the largest life science membership organization in the world, with over 43,000 members (and more than one third of them, like myself, are located outside the United States). General meetings, held once a year, are huge events with over 10,000 attendees, and cover new research related to the biology of microbes.

The latest general meeting took place in San Diego (May 23-27), and I tried to follow the event as closely as possible through the internet. Good for me: many attendees shared their thoughts, in real time, using social media. Also, and I think this is praiseworthy, the ASM actively used a battery of social media channels, and broadcasted on the internet several live interviews with selected scientists. And all this internet activity was freely available to anyone.

During those days, I followed the messages that the ASM and the attendees posted on Twitter, the popular microblogging service. To do this, I didn't need to know who was attending the meeting -- I just searched for Twitter messages (a.k.a. tweets) containing the following tag (or hashtag) that was chosen beforehand by the organizers: #asmgm (abbreviation for "ASM general meeting"). In the simplest way, this can be done using the "search" function of Twitter, as you can see if you click here (but note that tweets older than a few days are not retrieved).

So, when somebody wanted to post a tweet related to the ASM meeting, they just added the #asmgm hashtag, as in this example:

The tweet was written by science writer Carl Zimmer, and was one of the most retweeted messages during the meeting. It referred to a talk entitled "The biochemistry of beer" being given at that precise moment by Charlie Bamforth, a professor from the University of California, Davis.

Other Twitter messages posted by meeting attendees were also retweeted many times. I wonder how far the #asmgm tweets reached, having in mind that some of the twitterers at the ASM meeting had many hundreds of Twitter followers (e.g. Carl Zimmer has over 18,000)... Is there a practical way to calculate the total audience that a single tweet has had during a certain period? I don't know -- but I'm pretty sure that the room where Charlie Bamforth gave his "beer talk" wasn't big enough to hold all the people who read his "mustache quote" on Twitter.

Another memorable quote from the ASM meeting was:

The quote was pronounced by Edward DeLong, professor at the Massachusetts Institute of Technology, during his talk "Evolution and ecology in microbial ecosystems: unity in diversity." On a later tweet, Zimmer wrote: "Clarification of previous tweet/koan: genomes are not fixed. They are ever-changing, swapping genes, shuffling segments, mutating,etc."

Finally, another tweet by Carl Zimmer summarised a general idea that is common knowledge among microbiologists (or so I like to think) but might sound like news to many other people:

I'm not sure where the quote came from, as there were many talks going on at the same time (the meeting program has 350 pages, and that's without abstracts!). But it's clear that most types of bacteria on Earth are harmless to us. I would even say that most microbes don't even know that we humans exist... It's only because of our hard-to-eradicate anthropocentrism that we feel that microbes exist only to make us sick (and to provide us with beer, of course!).

But this blog post is getting very long, so I'm interrupting it here. The story about the ASM meeting and social media continues in my next post.

A Twitter view of the general meeting of the American Society for Microbiology - #asmgm

noreply@blogger.com (César Sánchez) — Thu, 03 Jun 2010 18:00:00 +0000

The above image is a word cloud generated from about 1200 tweets (that is, messages posted on the microblogging service Twitter). All these tweets are related to the general meeting of the American Society for Microbiology (ASM), which was recently held in San Diego, California (May 23-27).

Please wait for my next blog post, where I'm going to tell you about a few things that could be learnt about microbes by following the ASM meeting on the internet -- no matter your physical location on Earth (and beyond?). Also, I'm going to explain how I made the word cloud -- I'm pretty sure there must be a better and easier way to do this, so I would certainly appreciate your feedback on my next post.

Note: unfortunately, the tags in the cloud are not hyperlinked. The image was generated using Wordle.

Media for Science Forum: poor organization, disappointing use of social media

noreply@blogger.com (César Sánchez) — Thu, 20 May 2010 13:16:00 +0000

A science journalism congress was held last week in Madrid, Spain, under the name Media for Science Forum (MFSF). This was a European congress dealing "with strategic issues about science communication and science journalism and its social dimension." One of its specific objectives was declared to be: "Explore new trends in Science Communication due to the web 2.0".

Well, this sounded really exciting to me (and registration was free!), so I planned to attend the congress. Unfortunately, the organization rejected my application due to the huge amount of requests received.

So, I couldn't attend the meeting in Madrid --but I followed the events from my home at London, using the internet.

This post describes my personal experience of MFSF, including a few thoughts about the use of social media. You are more than welcome to add your comments at the end of the post.

March 18th

I first learnt about the upcoming Media for Science Forum (MFSF) through an announcement made on the SINC webpage (in Spanish). SINC (www.plataformasinc.es) is a news agency focused on scientific research done at Spanish institutions and research done by Spaniards at foreign institutions.

After visiting the MSFS official webpage, I filled and sent the online registration form the very same day. Registration was free but seats were limited: the organization would contact me in due time to accept or reject my application.

After registration, I was expecting to receive an email, automatically generated by the system, acknowledging my registration and providing some additional information --this seems a common procedure for online forms--, but this message did not arrive.

Anyway, I sent a tweet to inform my Twitter followers about the event, suggesting a possible hashtag. I also announced the conference on the Science Writers Facebook page.

April 4th

Over two weeks passed, but I didn't receive any email from the organization, and no new information was posted on the MFSF website. So I sent them an email including all my personal information and a link to my CV. I also explained them that I needed to know about the success or failure of my application in a short time, as I eventually had to make some arrangements for my trip London-Madrid.

April 6th

The MFSF organization forwarded me an email, which was supposed to be sent to me on March 18th (but I had not received). The message thanked me for the registration and informed that I'd be contacted again by the organization about the possible success of my application. When? "Soon." No more details were included.

April 7th

I received an email with the following request: "We have had problems in our system, and I have to ask you to reconfirm the dates that you are planning to attend the Forum".

The problem is that the email did not come from the congress organization but from a known Spanish travel agency. I checked the MFSF website (again) looking for some explanation or connection to this travel agency: I couldn't find anything. Anyway, I replied with the requested information: I planned to attend both days (12th and 13th May).

April 12th

MFSF started to use Twitter and Facebook!

I thought: "Great, they'll keep us informed about what's going on."

Oh, how wrong I was...

April 14th

New email from the travel agency, including a message from the MFSF organizers: they started a blog!

"Excellent, another channel to keep in touch with us! Now we'll get some news!" -- or so I thought.

I wasn't sure if that message meant that my application had been successful, so I requested some information about it. They replied immediately: "Nobody is receiving any confirmation. The organizers are still receiving applications, and they haven't made any decisions yet. We will inform you in due time" (my Spanish-to-English translation).

April 28th

During the previous days I had exchanged a few messages with other members of a LinkedIn group (Periodismo científico y divulgativo, which is Spanish for "Science journalism"), and learnt that nobody seemed to have received any confirmation regarding their MFSF application.

So I posted a message on the MFSF Facebook page, requesting information (to see my message there, you need to click on "Media for Science and others", as the default page only shows messages written by the organizers).

They never replied to my message on Facebook.

April 29th

Six weeks after my registration, and 13 days before the event, the MFSF organizers sent me an email: "Unfortunately your request to participate on the congress has been denied due to the huge amount of requests received."

You can imagine this didn't make me very happy.

Anyway, I still expected to know more about the MFSF talks and discussions through the internet, by making use of social media.

May 12th: first day of the congress

Early in the morning, I learnt from Twitter (actually, I think it was through this Topsy search) that the MFSF talks were going to be broadcasted through live web streaming.

Oh, wait, it appeared that only the opening talk was to be transmitted.

Note that I didn't get that information thanks to MFSF "Web 2.0" tools: their blog, Twitter and Facebook pages were all mute about this issue at the time (and even later).

The opening talk --the only one that was to be live streamed-- was untitled and in charge of the General Director of FECYT (Spanish Foundation for Science and Technology). This didn't sound very exciting to me. So, I forgot about MFSF for the rest of the day. My plan was to check the internet for related discussions on the following days.

May 13th: second and last day of the congress

At midday, I was surprised to know (through Twitter, but not MFSF Twitter) that the forum broadcast was still live!

Although with some interruptions in the service, they had been transmitting the whole thing!? Apparently, this was just an unplanned, happy idea. Well, I guess nobody had thought about this possibility before...???

Anyway, so I was able to watch the afternoon talks. These included brief descriptions of European scientific news services (such as AlphaGalileo), and the final conclusions (which were not such a thing but a list of general recommendations). Nice, but not incredibly useful.

Today, May 20th
Today I've been searching the internet, including Twitter, for reactions to MFSF (see links below). It seems that the congress was quite popular on Twitter: the hashtag #mfsf (not the one I suggested) became the second trending topic on Twitter in Spain. That's pretty good for a science journalism congress!

...Although it must be said that many tweets were messages of the lifecasting type ("On my way to Madrid...", "Having a beer in...", and the like), which in my opinion only contribute to the noise -- when they are tagged with a congress hashtag.

From what I can read on the internet, it seems that most people found the forum interesting -- too bad my application was rejected. On the negative side, MFSF was poorly planned, and failed to provide essential information to potential attendees and the general public.

In particular, their use of social media (blog, Facebook, Twitter) for updates and conversation was really disappointing -- and remember that one of their specific objectives was to "explore new trends in science communication due to the web 2.0". After the first hello message, MFSF published only 10 messages on Twitter and 13 updates on Facebook (numbers correct at the time of writing this) -- and all these messages were just announcements of new blog posts. No updates about registration issues, no announcements concerning the live web broadcasting, no comments on specific talks, no conversation at all. That is useless to me.

Reactions to MFSF:
- No hay que ser innovador... tan sólo parecerlo [in Spanish] by Javi Peláez. La aldea irreductible, May 12th, 2010.
- Media for Science Forum (1), (2) and (3) [in Catalan] by Miquel Duran. Edunomia, May 12-13-14, 2010.
- Media for Science Forum and (II) [in Catalan] by Pep Anton Vieta. Pepquímic, May 12-15, 2010.
- Media for Science Forum 2010 – ein Rückblick [in German] by Hans-Dieter Zimmermann. FHS eSociety Blog, May 18th, 2010.
- El estado del periodismo científico, en el Media For Science Forum de Madrid [in Spanish but with English introduction] by Pere Estupinyà. Knight Science Journalism Tracker, May 19th, 2010.

My selection of YouTube videos related to the microbial world

noreply@blogger.com (César Sánchez) — Fri, 14 May 2010 12:55:00 +0000

During the last couple of years I've been collecting some YouTube videos related to microbiology. My microbiology playlist includes now over 70 videos of very different styles, including not only academic lectures and documentaries, but also animated movies and funny songs.

You can watch many of these videos using the embedded viewer (see below).

Or, you can watch all of them on my YouTube channel. You will find there other playlists, including:
- Microscopy
- Molecular and Cell Biology
- Other sciences

Please let me know if you find any of the playlists useful or, at least, entertaining.

Uncovering beauty in proteins to fight the pneumococcal fratricides

noreply@blogger.com (César Sánchez) — Wed, 05 May 2010 12:06:00 +0000

This post is about pneumonia and pneumococci, fratricide at the cellular level, and a pretty protein. And there's a video too!

First things first. Pneumonia is a common disease characterized by inflammation of the lungs that can be deadly: 4 million people in the world die from it every year. Half of them are children under 5 years of age -- in fact, no other illness causes more deaths of children under age 5 worldwide. However, this is a preventable and treatable disease in most cases.

Many organisms can cause pneumonia, but the usual culprits are the bacteria Streptococcus pneumoniae (or pneumococcus, see above image) and, less frequently, Haemophilus influenzae type b (a.k.a. Hib). Safe and effective vaccines and antibiotics have been developed for these infections. Unfortunately, they are not commonly available in most developing countries, where pneumonia allies with poor nutrition, other illnesses (e.g. AIDS) and lack of resources to contribute to the cycle of poverty. To know more about the impact of pneumonia on world health and what can be done about it, I recommend listening to this podcast and visiting the World Pneumonia Day website.

My only direct contact with pneumococcus research was... hum... many years ago. As an undergraduate student, I spent two months at the Centro de Investigaciones Biológicas (CIB, Center for Biological Research) in Madrid, Spain, where I learnt how to cultivate pneumococci and some techniques for the study of lytic enzymes. These remarkable enzymes play a key role in bacterial physiology by cleaving, in a regulated fashion, specific linkages in peptidoglycan (that is, the highly cross-linked polymer that forms the bacterial cell wall). This apparently destructive activity is essential for cell wall turnover, and allows cell growth and division. Interestingly, the genomes of some bacteriophages (or bacterial viruses) also encode lytic enzymes, which the viruses use to break the cell wall and escape from its dying host after viral replication. These enzymes could be useful as antibacterial agents.

A few days ago I was happy to learn that a group of Spanish researchers --some of them from the CIB-- had solved the 3D structure of one of the pneumococcal lytic enzymes, called LytC. What I find remarkable is how the 3D structure elegantly explains the peculiar role that this protein plays during a process known as pneumococcal fratricide.

Some bacteria produce substances that kill surrounding microbes, and use the resulting dead bodies as a source of nutrients. Sometimes, killer and victim belong to the same species, or even they are siblings. In these cases, researchers speak of cannibalism or fratricide; although if you view microbial populations as coordinated, multicellular entities, then you may prefer to use the term programmed cell death.

Among pneumococci, some cells in a population become competent in response to certain signals; which means that they are able to take up DNA from their surroundings, and incorporate this genetic information into their own chromosome. This way, competent cells can acquire new inheritable abilities -- such as production of a new capsule type, or resistance to an antibiotic -- that can be very important for their survival (this was the underlying mechanism in the famous Avery-MacLeod-McCarty experiment that helped identify DNA as the hereditary material in cells).

But competent pneumococci do something else: they encourage non-competent siblings and other closely-related bacteria to commit suicide. They do this by releasing a particular lytic enzyme, called CbpD, that diffuses through the milieu and --somehow-- activates LytC and other lytic enzymes that are already present in the non-competent siblings. Cell wall weakening finally results in a big bang; that is, the explosion of the non-competent pneumococci. The materials released serve not only as nutrients and sources of genetic information (DNA), but also as virulence factors that help competent cells to survive in their human host.

The 3D structure of LytC now provides the clues to explain the enzyme's peculiar behaviour during pneumococcal fratricide. Have a look at the model of LytC on the left: ain't it a beauty? A substrate-binding module (in blue and green in the image) recognizes and binds the cell wall peptidoglycan, whereas a catalytic module (in red) is responsible for breaking a specific linkage in the substrate. Because of the unusual hook shape of the protein, the substrate-binding module and the catalytic module partially block each other. As a result, LytC cannot bind the highly cross-linked peptidoglycan that is predominant under normal circumstances. Only when CbpD or other lytic enzymes cut specific linkages in the cell wall, LytC is able to bind the 'loosened' peptidoglycan and comes into action -- with deleterious consequences for the non-competent pneumococci.

To make the story even more attractive (at least to me), the researchers bothered to produce a video that illustrates -- in a fascinating way -- the pneumococcal fratricide and the mechanism for LytC activation. Please watch it, the background music is nice too. The video includes some captions in Spanish, but I uploaded the video to YouTube and added English subtitles for a wider audience. I hope more researchers will get into the trouble of making visually attractive videos or presentations of their work (and make them freely available), it really makes a difference...

I also add here a nice composite image from the press release, just because I think it's so beautiful:

Reference for the 3D structure of LytC:
Pérez-Dorado, I., González, A., Morales, M., Sanles, R., Striker, W., Vollmer, W., Mobashery, S., García, J., Martínez-Ripoll, M., García, P., & Hermoso, J. (2010). Insights into pneumococcal fratricide from the crystal structures of the modular killing factor LytC Nature Structural & Molecular Biology DOI: 10.1038/nsmb.1817

Recommended links:
- World Pneumonia Day (November 12th).
- Keith Klugman - Pneumonia: the hidden giant. In this podcast, Carl Zimmer interviews Keith Klugman, Chair of Global Health at Emory University, USA.
- Klugman's crusade by Valerie Gregg. Public Health Magazine, Emory University, spring 2006.
- Neumococos fratricidas [in Spanish], noticia publicada en la web del CSIC (20 de abril, 2010).
- Los neumococos fratricidas [in Spanish]. RTVE.es (20-04-2010).

Other relevant scientific articles:
- Bacterial programmed cell death and multicellular behavior in bacteria [free article] by Hanna Engelberg-Kulka et al. PLoS Genet. (2006) 2(10): e135.
- Cannibalism and fratricide: mechanisms and raisons d'être by Jean-Pierre Claverys & Leiv S. Håvarstein. Nat. Rev. Microbiol. (2007) 5: 219-29.
- Bacteriophage lysins as effective antibacterials [free article] by Vincent A. Fischetti. Curr. Opin. Microbiol. (2008) 11: 393–400.
- Pneumococcus: the sugar-coated bacteria [free PDF] by Rubens López. Intl. Microbiol. (2006) 9: 179-190.

Image sources:
- Streptococcus pneumoniae in spinal fluid. FA stain (digitally colorized). Content Providers(s): CDC/Dr. M.S. Mitchell. Source: Wikimedia Commons.
- World Pneumonia Day logo.
- Nature Structural & Molecular Biology cover, May 2010, Volume 17 No 5.
- LytC model, LytC and pneumococci: both images from press release, CSIC.es

Elio Schaechter comments on state microbes at NPR (podcasts)

noreply@blogger.com (César Sánchez) — Fri, 30 Apr 2010 09:37:00 +0000

It seems that Wisconsinites are not getting their own state microbe after all. What a shame!

Transcripts of these radio podcasts are available at the NPR website:
- A state microbe for cheese-crazed Wisconsin? April 16th, 2010.
- No state microbe for Wisconsin. April 28th, 2010.

From Wikipedia:

National Public Radio (NPR) is a privately and publicly funded non-profit membership media organization that serves as a national syndicator to 797 public radio stations in the United States.

NOTE added on May 7th, 2010:
For a thorough list of candidate state microbes, see State Microbes at Small Things Considered, May 6th, 2010.

NOTE added on October 11th, 2010:
More suggestions (including several streptomycetes) by Joan W. Bennett & Douglas Eveleigh (Rutgers, The State University of New Jersey): State Microbes, Microbe magazine, October 2010.

"Hope he's only a Sunday creationist" by G. Trudeau

noreply@blogger.com (César Sánchez) — Tue, 20 Apr 2010 10:01:00 +0000

This comic strip by Garry Trudeau was published in 2006, so you may already know it. Here, a doctor offers two antibiotic choices to a patient suffering from tuberculosis (TB). The choice appears to depend on the patient's religious beliefs. I hope the patient chose wisely -- for his own benefit and for that of all the people that could be otherwise infected by his spreading of TB microbes.

Interestingly, cartoonist Garry Trudeau is the great-grandson of Dr. Edward Trudeau, who founded the Adirondack Cottage Sanitarium for the treatment of pulmonary TB, at Saranac Lake, New York State, in 1884. It was found at the time that tuberculous patients greatly benefited from a "rest cure" that included lots of mountain fresh air, and good nutrition. The sanatorium was later renamed and reorganized as a biomedical research center. Known today as the Trudeau Institute, it is devoted to researching our immune system to find better ways of preventing and treating human diseases, including TB, influenza, tropical diseases and cancer.

Credits for images:
- Cartoon:
Author: Garry Trudeau (Doonesbury.com). Source: GoComics.
- Stamp:
United States Postal Service. Stamp designed by Howard E. Paine and created by Mark Summers, based on a photograph of Dr. Trudeau provided by the American Lung Association. Source: The Stamp Collecting Round-up. See also a press release at EurekAlert.

Hat tip:
Comunicar ciencia con humor [in Spanish] by José Pardina, Asociación Española de Comunicación Científica (AECC) [Spanish Association for Science Communication].

Social media for microbiology education and research

noreply@blogger.com (César Sánchez) — Mon, 12 Apr 2010 16:41:00 +0000

Vincent Racaniello is a well-known Professor of Microbiology at Columbia University Medical Center, New York. As a complement to his research and his classes on virology, he successfully uses different social media tools (blogging, podcasting, microblogging) to spread the love for viruses -- I mean, to teach the public about viruses (the kind that make you sick... or not).

The following video is a recording of a great talk he gave at the Spring 2010 meeting of the Society for General Microbiology in Edinburgh, UK. In this presentation he explains -- in simple terms -- how he uses blogging, podcasting, and other social media tools for the popularization of virology.

I'm wondering if the talk could convince a few of the microbiologists in the audience to jump on the social media bandwagon...? Anyone?

The video is licensed under a Creative Commons Attribution license, and can be watched also at BioCrowd or at Virology Blog.

Image credits: "Jump on the social media bandwagon" by Matt Hamm. Source: Flickr. Image used under an Attribution-Noncommercial Creative Commons license.

Beauty contests for promoting science?

noreply@blogger.com (César Sánchez) — Thu, 08 Apr 2010 10:03:00 +0000

I was browsing the printed edition of a local newspaper (for a London borough), and a brief story caught my eye: Top genes expert is UK Miss India.

To be honest, I had to read the headline twice to grasp its meaning. "Top genes expert" is not a very common expression (actually, I searched Google and found no results, which is remarkable these days!). And "UK Miss India" was also a little confusing to me... but it may be just me.

The story was about a local resident who happened to win a beauty contest. Nothing special here -- lots of pretty people live in my neighbourhood :) . What caught my attention was that the beauty queen works as "a stem cell researcher at Imperial College Healthcare Trust." At the official Imperial College website I found that she is a professional model and actress, and "she intends to spend her reign promoting science and medicine, while undertaking community projects."

First I should say that I admire anybody who does research and, at the same time, is engaged in a different activity in a professional way (not just as a hobby). I wasn't capable to do that in my research days.

Anyway, I used to think that beauty contests and science popularization were two unconnected issues. But now I'm not so sure. Science can be promoted in many different ways...

Perhaps a modified version of today beauty contests could be used for the promotion and popularization of science.

What do you think? Do you know of any examples of this, or anything similar?

Somewhat related links:
- Science Babes and Science Hunks. I, Science (a science magazine for Imperial College), 15th January 2010. A list of sexy scientists in cinema.
- Sexy Science- "a look into the hottest science currently going on today and the hot scientists behind that work." Or so they say...
- Science Babe - "the science of everyday life". The first video, "The physics of high heels", is interesting. I'm curious about how this effort for science popularization will develop...
- We're scientists AND we're sexy! - a Facebook group.
- Sexy Science - stock photographic images. It seems that you may become a sexy scientist by wearing a white labcoat and big glasses, AND looking like an expressionless robot...
- Geeks are Sexy - "tech, science, news and social issues for geeks".

Beauty and sexiness are relative concepts. You may find this scientist pretty or attractive in some way...

Image credits: the science of fizz, by goopymart. This image is included here under an Attribution-Noncommercial-Share Alike Creative Commons license.

Tuberculosis and AIDS: two diseases, one response

noreply@blogger.com (César Sánchez) — Wed, 24 Mar 2010 18:50:00 +0000

Today is World TB Day, an excellent time to watch the following video (available at the World Health Organization YouTube channel):

You can read about the current state of the disease -- which kills almost two million people every year -- here: A world free of TB (Word Health Organization).

You can also watch a few more videos on the topic at Stop TB Partnership. I especially recommend two videos:
- Actions For Life - A flash film about the Global Plan to Stop TB
- The Human Face of TB, an informational flash film

I'll finish the post with some words written by Margaret Chan, WHO Director-General:

"If the right action is not taken right now, the continuing spread of MDR-TB [multidrug-resistant tuberculosis] could transform a disease that is curable with affordable medicines into a costly and deadly epidemic. If the right action is not taken right now, the continuing rise of XDR-TB [extensively drug-resistant tuberculosis] could take the world back to the era that predates the development of antibiotics, with nothing in hand to guarantee treatment success."

"The microbial world has given us a clear either-or situation. Either we tackle the problem now with rational and proven approaches, or we pay later with an epidemic of an airborne disease that renders our modern-day medicines and straightforward treatment regimens obsolete. This would truly be a tragedy, on a huge and costly scale, that should not happen."

Related links:
- World TB Day. Twisted Bacteria, March 24th, 2008.
- An 'open source' approach to drug discovery. Twisted Bacteria, July 1st, 2008.
- Robert Koch y la tuberculosis. En Días Como Hoy, RTVE.es , 24 de marzo, 2010. [In Spanish] Se trata de un fragmento de un programa de radio (dos minutos y medio) en el que Nieves Concostrina nos recuerda, de forma amena, el momento en que el gran Robert Koch presentó al mundo la bacteria causante de esta enfermedad ("su bacilo").

Year of Biodiversity: only for cute animals and plants?

noreply@blogger.com (César Sánchez) — Wed, 17 Mar 2010 20:05:00 +0000

The United Nations declared 2010 to be the International Year of Biodiversity. This sounds great, let's celebrate and protect the variety of life on Earth! We must learn more about current (and past) biodiversity and the impact that human activities have on the distribution and abundance of organisms. Also, we should explore any effective ways to protect biodiversity, if only because it benefits us.

However, it strikes me as short-sighted that most biodiversity advocates seem to care only about "the cute organisms" (cute by most human standards, I guess); that is, a few particular animals and plants. But... for Pete's sake, life on Earth goes well beyond a few vertebrates, trees and corals! Surprisingly, the true diversity of life is not obvious at all in the writings of most biologists, conservationists or environmental scientists when discussing biodiversity and its protection.

I know, I know -- when a clear message is to be delivered to the general public, you cannot be comprehensive. If you can mention only a couple of examples for endangered species, you better go for the much-like-us mammal, or the colourful bird, or the pretty tree or flower. Most of us can easily sympathize with a chimpanzee (that is, really, almost one of us) or with many animals: they have faces, with two eyes and a mouth, and it's hard not to see part of our own reflection there. We often show emotional responses also to trees, flowers or grasses (even mushrooms). So, when explaining the importance of biodiversity to a general audience, sticking to the cute guys might be the wise choice.

But how is this topic treated inside the scientific community? Well, in general, I don't see much difference. When biodiversity is discussed -- in general terms -- in scientific articles, editorials or websites, the focus is again on certain plants and animals that can be seen by the unaided human eye (that is, macro-organisms). By contrast, microbes are hardly ever referenced, if at all.

Why are microbes not even mentioned most of the times? Why are some particular organisms (let's call them "the cuties" for short) the focus of research and protectionist efforts? I can think of a few possible answers:

1 - The cuties, among all the living beings, might suffer the highest risk of extinction.
2 - Although there are other organisms at higher risk, the cuties are perhaps more important (in some way) either for the preservation of particular ecosystems or for human well-being.
3 - Our current knowledge of life diversity might be very limited, and is focused on particular organisms because of historical and technical reasons.

I guess that most scientists and many learned people would agree with me that answer number 3 seems about right (but if you think otherwise, please leave a comment). Actually, it seems that we know very little on the matter. Scientists are starting to agree -- I think -- on a broad definition of biodiversity. But the field faces (at least) two huge challenges. First, there are many organisms living on (and inside) this planet that we haven't met yet, and our estimates of how many species are awaiting discovery are little more than educated guesses. Second, although biodiversity can be measured at various levels, it's often understood as referring to the number and relative abundance of different species. And deciding if two organisms belong to a single species, or to two different ones, can be really hard. Moreover, the difficulty in agreeing on species definition depends greatly on the type of organism it applies to: whereas this issue causes some serious troubles when studying cuties, it appears almost insurmountable when trying to define microbial species. Why is this so? Well, I'm not getting into this here, but let's say that the species concept was originally created and crafted for the cuties, and microorganisms just don't fit into such clothes.

However, even lacking a suitable species definition (to the embarrassment of microbiologists), we can confidently say that the microbes are much more diverse than the cuties. This diversity is shown at different levels: genetics, biochemistry, ecology... You can find microbes almost everywhere, and often in amazingly high numbers. No matter if you count individuals or you measure biomass: microbes are the (silent?) majority. Some microorganisms are essential not just for the preservation of particular ecosystems but for the continuity of life on Earth as we know it (and when I write "life" I mean "life", not just "cuties"). Under any non-human-centred point of view, life is microbial -- with a few exceptions, yes.

So, just to recapitulate... Some animals and plants appear to be on the brink of extinction because of human actions, and it doesn't seem a good idea to let them go. However, we don't know how many types of organisms are out there, or how many of them are endangered by our activities, and we don't understand the long-term effects of the extinction of any particular life form. Yes, more research is definitely needed.

But we do know that life is incredibly diverse and mostly invisible to the human eye, and that the cuties are not even the tip of the iceberg. So, any serious research or scientific communication on the diversity of life should include (in my opinion) some mention to microbes, the main actors on this movie -- at least we should acknowledge our ignorance! Microbes play key roles in nature: shouldn't we worry about the preservation of microbial diversity?

Don't get me wrong: I don't want any cuties to become extinct. But I think that scientists can do a much better job when discussing biodiversity.

Further reading:

If you find the topic of this post interesting, you must read the following excellent articles written by Sean Nee, University of Edinburgh, UK (articles can be downloaded from the author's website):

- The great chain of being. Nature (2005) 435: 429.

"Our persistence in placing ourselves at the top of the Great Chain of Being suggests we have some deep psychological need to see ourselves as the culmination of creation."

- Extinction, slime and bottoms. PLoS Biology (2005) 2(8): e272.

"There is an old Chinese curse: ‘May you live in interesting times.’ According to those who know about such things, we live in a momentous time, the time of the Sixth Mass Extinction! But most of us do not feel at all cursed. Because, in fact, the Sixth is quite different to the previous Big Five—no-one would notice this one if we were not repeatedly reminded of it by ecologists."

- More than meets the eye: Earth's real biodiversity is invisible. Nature (2004) 429: 804-805.

"We are still at the very beginning of a golden age of biodiversity discovery, driven largely by the advances in molecular biology and a new open-mindedness about where life might be found. But for this golden age to be as widely appreciated as it should, our view of the natural world must change — as radically as did our view of the cosmos when we began looking at it with technologies that allowed us to see more than can be seen with the naked eye."

- Beyond the tangled bank (pdf). This manuscript seems a slightly longer version of More than meets the eye: Earth's real biodiversity is invisible. Interestingly, it includes many references that were not incorporated into the published article.

I also recommend a thought-provoking article by Maureen A. O’Malley & John Dupré, University of Exeter, UK:

- Size doesn’t matter: towards a more inclusive philosophy of biology. Biology and Philosophy (2007) 22, 155-191.

NOTE added on April 17, 2010:
A Letter has just been published by Andrew Beattie and Paul Ehrlich in Science, highlighting what The Missing Link in Biodiversity Conservation is:

"the many millions of species within the numerous phyla of microbes and invertebrates, which represent perhaps 95% of total species and genetic biodiversity."

The authors propose to deliver a new message to the public:

"a new message, one we would like to label "production biodiversity": By protecting microbes and invertebrates, we also protect the primary industries upon which we all depend."

I agree!

Related links:
- (Added April 20, 2010) A commentary on the same subject has been published by Mercè Piqueras in her blog, La lectora corrent (in Catalan): La biodiversitat invisible.

- (Added June 23, 2010) See Dear New Scientist by Ed Rybicki, who reminds us that "the greatest part of the biodiversity on this (and probably any other) planet is viruses."

- (Added August 19, 2010) Preserving endangered species – of gut microbes, by Grant Jacobs. Or the need to preserve the human gut microbes found in ancient rural populations.

- (Added September 11, 2011) Bacteria & archaea don't get no respect from interesting but flawed #PLoSBio paper on # of species on the planet, by Jonathan Eisen.

- (Added September 11, 2011) Don’t forget to count microbes, by David Hooper & Bonnie Bassler.

Edward Jenner and Joseph Lister, posted

noreply@blogger.com (César Sánchez) — Mon, 08 Mar 2010 20:20:00 +0000

A few days ago, the UK postal service issued a new series of stamps featuring 10 eminent scientists to celebrate the 350th anniversary of the Royal Society. The image above shows two of the stamps, depicting Edward Jennner (1749-1823) and Joseph Lister (1827-1912) -- who are considered the 'fathers' of vaccination and antiseptic surgery, respectively. They both had a rough time trying to convince their fellow physicians to accept their proposed methods as good and useful practices. But they eventually succeeded, and millions of lives were saved.

It is noteworthy that Jenner was elected a fellow of the Royal Society in 1789 thanks to his research on cuckoos (the birds, not the clocks). He was a 'natural scientist' and studied a variety of issues ranging from fossils to animal behaviour, and from balloons to medicine. It was in 1796 when he carried out his famous experiments, showing that people could be protected against the deadly smallpox by inoculating them with cowpox (a mild, related disease). Although the basic rationale behind Jenner's technique was not novel (but this was not the reason why the Royal Society rejected his original report!), his careful studies and his tenacity were fundamental for a wide progressive adoption of vaccination. Now --two centuries later-- the world can celebrate the 30th anniversary of smallpox eradication. This deserves a stamp or two, doesn't it?

Now, let's turn our look to Joseph Lister. He introduced phenol (carbolic acid) to sterilise surgical instruments and to clean wounds. As a result, post-operative infections were greatly reduced, and many lives (and body parts that otherwise would be amputated) were saved. Because of these achievements, Lister was not only elected fellow but president of the Royal Society (between 1895 and 1900), and his name was given to a bacterium ...and a mouthwash (what an honour!).

Anyway, it seems that there was some kind of infectious hunger for 'small knowledge' at the Listers' house, as Joseph was not the only one interested in the microscopic world. His father, Joseph Jackson Lister (1786-1869), made crucial advances toward correcting image aberrations in microscopes (and he was elected fellow of the Royal Society in 1832). After his work, the improved microscopes became powerful instruments, allowing more detailed observations of specimens and, hence, the birth of modern histology.

Now this may not come as a surprise to you, but (at least) two other members of the family were also elected fellows of the Royal Society. They were Arthur Lister (1830-1908, Joseph's brother) and Gulielma Lister (1860-1949, Arthur's daughter). Arthur and Gulielma became renowned botanists and mycologists, and world experts in mycetozoa (myxomycetes, slime molds). I'm wondering if they started by playing with J.J.'s old microscope? Gulielma's achievements are especially remarkable in a time (early 1900's) when very very few women were allowed to excel in science: she was a founding member of the British Mycological Society (and president in two occasions), as well as fellow, council member and vice-president of the Linnaean Society. Does anybody know of a stamp featuring Gulielma? Probably not (yet) but this could be a good topic for the next International Women's Day...

Further reading:

Stamps commemorating the Royal Society anniversary:
- Getting the Royal Society stamp of approval by Charlotte King. New Scientist, 25 Feb 2010. It includes large-size images of the 10 stamps.
- The Royal Society 350 Years, British Postal Museum & Archive.
- Science stamps mark the Royal Society's 350th anniversary, Royal Society, 24 Feb 2010.
- 350th Anniversary of the Royal Society, new Great Britain stamps, Norvic Philatelics. Includes interesting technical details and image credits, and a few special postmarks.

Edward Jenner and smallpox:
- Edward Jenner Museum, Gloucestershire, UK. Excellent website with plenty of information.
- Edward Jenner and the history of smallpox and vaccination by Stefan Riedel, Proc (Bayl Univ Med Cent) (2005) 18, 21–25.
- Edward Jenner (1749-1823), historical figures, BBC.
- Smallpox, World Health Organization.

Joseph Lister and his relatives:
- Joseph Lister: Surgery Transformed, a video produced by British Medical Journal Media.
- Joseph Jackson Lister (1786-1869), Pioneers in Optics. Science Optics & You, Molecular Expressions.
- Early Myxomycetologists (including Arthur and Gulielma Lister), Myxoweb.
- Gulielma Lister (1860-1949), biography, Wanstead Wildlife.
- Biography of Gulielma Lister (1860-1949), The Biographical Dictionary of Women in Science: L-Z. By Marilyn Bailey Ogilvie, Joy Dorothy Harvey.

Microbiology (and other sciences) featured on stamps:
- Microscopy on stamps by Dave Walker, Microscopy-UK. Great article, together with the following one:
- Photomicrography on stamps by Dave Walker, Microscopy-UK.
- Physics-related stamps, compiled by Joachim Reinhardt. Mostly about physicists, but there are also a few other scientists, mathematicians and engineers (including Antonie van Leeuwenhoek and Robert Hooke).
- Science and Technology on Stamps, A to Zee ("the web guide for collectors").
- Sci-Philately: a Selective History of Science on Stamps by Maiken Naylor, University at Buffalo Libraries.
- Medical Stamps, Scientific-web.com
- Filatelia Médica - Medical Stamps by Dr Tuoto.
- Pasteur on Stamps by Dr Tuoto.
- AIDS on Stamps.
- Malaria on Stamps Collection.
- Collect GB Stamps, resources for collecting British stamps. It has a good search tool.

The Poetry of Reality (An Anthem for Science)

noreply@blogger.com (César Sánchez) — Wed, 03 Mar 2010 19:24:00 +0000

I love this video. Please watch it.

From the YouTube page:

The Poetry of Reality is the fifth installment in the Symphony of Science music video series. It features 12 scientists and science enthusiasts, including Michael Shermer, Jacob Bronowski, Carl Sagan, Neil deGrasse Tyson, Richard Dawkins, Jill Tarter, Lawrence Krauss, Richard Feynman, Brian Greene, Stephen Hawking, Carolyn Porco, and PZ Myers, promoting science through words of wisdom.

Hat tip: Pere Estupinya.

Additional links:
- Symphony of Science, "a musical project headed by John Boswell designed to deliver scientific knowledge and philosophy in musical form."
- Symphony of Science - The Poetry of Reality (An Anthem for Science), with Spanish subtitles (con subtítulos en castellano)

Purple balloons and the secret of life: Génome at Genève

noreply@blogger.com (César Sánchez) — Wed, 24 Feb 2010 17:37:00 +0000

Lucky me, I am enjoying a few weeks with my partner in Geneva, Switzerland. During one of our first walks around the city, we noticed a big purple balloon on a small island in the Rhone river. Once we got closer (there is a bridge, no need to swim), we realized that this was no balloon --but a giant cell nucleus.

The bright purple dome, 14 meters in diameter, hosts an exhibition entitled Génome: voyage au coeur du vivant (Genome: a journey to the centre of life), or The secret of life (this subtitle appears on the English-version booklet).

Inside the dome --the cell nucleus-- we enjoyed a multifaceted, imaginative and colourful (even psychedelic?) introduction to genetics and the human genome: from Rosalind Franklin to genome sequencing, from DNA replication to dimples. But let me quote from the first page of the booklet, where the purpose of the exhibition is clearly described:

Dear VISITOR

We would like to take a minute
of your time to explain that

AN EXHIBITION IS FICTION

The wonderful world of the genome, which you will discover here, is an interpretation of reality. A purely scientific explanation could be difficult to understand. On the other hand an over-simplified one would not do justice to the astonishing ingenuity of nature.

You are about to enter a complex universe which is invisible to the naked eye. By using comparison and metaphor, a touch of poetry and humour, we hope that you will be both entertained and informed.

Please remember this message because it is true of all exhibitions; they are all interpretations of reality to a greater or lesser degree.

What an excellent description of what science communication to the general public should be! A delicate balance between (boring?) scientific information and (useless?) entertaining.

Did the Génome organizers accomplished their purpose? Well, they did it for us. You still have till February 28th to judge for yourself but, if you cannot make it to Geneva in time, the following video may give you a vague indication of what's going on inside the purple nucleus:

Génome: voyage au coeur du vivant has something for everyone. Science geeks may especially enjoy the awesome animations created by Drew Berry (including the one projected on the 360-degree screen over our heads!). Perhaps the name of this biologist and animator from the Walter & Eliza Hall Institute of Biomedical Research, Australia, does not ring a bell with you. But I'm almost certain that you have seen some of his award-winning films. See, for instance, the following selection:

The Génome booklet ends with some interesting "food for thought":

Perhaps we should take a philosophical view and agree that, in order to live life to the full, we humans will always need uncertainty!

Well put. And this goes far beyond genetics and evolution...

Links:
- Génome: voyage au coeur du vivant, exhibition webpage (in French), Université de Genève. It contains videos, photos and additional information.
- Genome: a journey to the centre of life, Swiss National Science Foundation.
- WEHI-TV, where you can watch and download several animations created at the Walter & Eliza Hall Institute of Biomedical Research, Australia. Titles include: Body Code, Immunology, Malaria Lifecycle.
- YouTube channel of the Walter & Eliza Hall Institute.
- Drew Berry, biomedical animator, CGSociety (Society of Digital Artists).
- An interview with Drew Berry at SeedMagazine.com

Image credits:
Festival Arbres & Lumières Geneva 2009. Île Rousseau with the Genome exhibition dome. Photo by Alejandro Pérez.